Every time I choose the wrong saved audio device, I cringe because I know I'm going to get not one, but two pop-ups -- and one of them is modal, so it's absolutely required to dismiss it first.
That is, 99 times out of 100 when I make a Jack configuration error (such as, I had been using a USB audio card, but then I went somewhere else and forgot to switch to built-in), I already know what the reason is so I don't need to see a large window with the full log. When this pops up, I just want to close that window and deal with the situation -- but I can't just close it, because a modal dialog is blocking the interface.
I would love to see a checkbox somewhere in the preferences that would allow one or both of these windows not to appear for every startup error. (I'm not suggesting to fail silently -- just that the current failure feedback is overbearing.)
At least in my use cases, in almost every case, it would be enough to put up a simple box with the error message, and allow that to be dismissed by the keyboard.
If I get an unusual error and I need to look at the log to investigate, I don't mind opening Messages by hand. But this is a rare case and, over time, it gets really irritating to have to keep closing a window that I hadn't requested, when a vast majority of the time I don't need that window to tell me what happened.
this can all be mitigated if you use the system-tray icon if supported by your desktop environment (big no-no if it's gnome3, sorry).
that way the annoying modal message box is replaced with a modeless notification bubble and you then can close the messages window as soon as it pops-up.
hth.
cheers